Summer course in analysis of high throughput data for population genetics 2024
General info
Date: August 19-23, 2024
Place: Copenhagen Denmark
Organized by: The Department of Biology, University of Copenhagen
Price: Free for all PhD students at Danish universities. 200 Euro for all other students.
Includes: All teaching. Food and accommodation are NOT included in the course fee.
Sign up: CLOSED for general registration Dispensation can be given to UCPH phd students
Contact: For questions write to cphsummercourse@gmail.com
Credit and diploma: The course is 4 ETCS credits and you will recieve a diploma
github with code
Content
The course is a comprehensive introduction to a number of topics and common research tools used in analyses of next-generation sequencing (NGS) data. Topics include: genetic drift, natural selection, population structure, recent and ancient admixture, spatial genetics, f-statistics and demographic inference and simulations. We will cover the theoretical concepts but the main focus is practical use of the methods. Lectures will be combined with hands-on computer exercises.
Intended Learning Outcome
After the course the student should be able to:
- Use population genetic theory to infer basic population genetics characteristics from genetic data
- Be able to infer ancestry and population structure based on genetic data
- Use NGS data including low depth for population genetic inference.
- Select the optimal strategy for selection scans depending on the population genetics characteristics of the sample population, including taking population structure into account
- Interpret and discuss the results of own analyses and results in the scientific literature
Instructors
Cindy G. Santander
My current research focuses on detecting strong but very brief selection, such as epidemics, using temporal and ancient genetic data. More broadly I am interested in health and disease within the context of human evolution and host-pathogen interactions. website
Garrett Hellenthal
Works on constructing and applying statistical methods to infer human history using genetic data. website
Shyam Gopalakrishnan
Population and statistical genetics website
Martin Sikora
Human and pathogen evolution. The Sikora group works at the intersection of ancient genomics, population genetics and paleoepidemiology and investigates the evolutionary history of humans and our associated pathogens. website
Ida Moltke
he research in my research group is focused on developing and applying statistical and computational methods to genomic data to solve problems in both population and medical genetics. Within population genetics we are mainly interested in trying to gain insights into how the human species has evolved and how the world was peopled. Within medical genetics we are mainly interested in identifying genetic variants that play role in a number of different diseases and traits, such as type 2 diabetes. website
Fernando Racimo
We are interested in using population and quantitative genetics to understand past evolutionary processes, with a particular focus on human evolution and ancient DNA. Our projects include developing tests to detect patterns of ancient selection, creating methods to integrate functional and population genomic data, and inferring demographic parameters using present-day and archaic human genomes. website
Anders Albrechtsen
Our group develops statistical and computational methods for analysis of genomic data website
Time and place
The course will take place from Monday August 19 to Friday August 23rd 2024 at Biocenteret, Ole Maaloes Vej 5, 2200 Copenhagen N. All lectures and computer exercises will take place in room 4.0.02 (i.e. building 4, ground floor, room number 2). This includes research talks. You can enter the buiding from two sides as shown shown on this map. Laptop
You should bring a laptop to the course. We will log into a remote server from the laptop so any laptop will do regardless of operating system. Course material
The lecture will be based on a large amount of reading material (articles/notes) that should be read in advance - you can find them here once they are finalized (you will get an email with password). The slides used during the lectures will be made available right before the lectures.
Program (Preliminary)
Monday - Introduction to population genetics and NGS data
09:00 - 09:15 Welcome (Ida Moltke)
09:15 - 10:15 Lecture 1: Introduction to basic population genetic terms and concepts (Fernando Racimo)
10:30 - 12:00 Computer exercises I
12:00 - 01:00 Lunch (on your own)
01:00 - 01:45 Lecture 2: Introduction to basic NGS data, Data processing, and formats (Anders Albrechtsen)
01:45 - 03:15 Computer exercises II ( break at 02.15)
03:30 - 04:15 Research lecture by Patrícia Pečnerová.
Using genomics to study the fine line between extinction and survival in mammoths and elephants
04:15 - 07:00 Reception/social mixer
Tuesday - Analysis of NGS data and population structure
09:00 - 10:15 Lecture 3: Estimation of allele frequencies, SNP calling and genotype calling from NGS data (Anders Albrechtsen)
10:30 - 12:00 Computer exercises III
12:00 - 01:00 Lunch (on your own)
01:00 - 02:15 Lecture 4: Population structure and admixture(Ida Moltke)
02:30 - 04:00 Computer exercises IV
04:15 - 05:00 Research lecture by Rasmus Heller
Genomes from the "Asian unicorn" reveal a long-standing decline
and two highly differentiated populations of saola
Canal boat trip
Wednesday - Population structure
09:00 - 10:15 Lecture 5: PCA in population genetics (Anders Albrechtsen)
10:30 - 12:00 Computer exercises V
12:00 - 01:00 Lunch (on your own)
01:00 - 02:15 Lecture 6: D/f statistics and ancient geneflow(Martin Sikora)
02:30 - 04:00 Computer exercises VI
04:15 - 05:00 Research lecture by Martin Sikora
Using population-scale ancient genomics to study ancestry,
social organisation and disease in Late Neolithic Scandinavia
Thursday – admixture graphs and selection
09:00 - 10:15 Lecture 7: Finestructure (Garrett Hellenthal)
10:30 - 12:00 Computer exercises VII
12:00 - 01:00 Lunch (on your own)
01:00 - 02:15 Lecture 8: Detecting genomic regions under (positive) selection (Cindy Santander)
02:30 - 04:00 Computer exercises VIII
04:15 - 05:00 Research lecture by Kristine Bohmann
Vacuuming animal DNA from thin air
Friday - Demography and simulations
09:00 - 10:15 Lecture 9: Dating admixture and selection in admixed individuals (Garrett Hellenthal)
10:30 - 12:00 Computer exercises IX
12:00 - 01:00 Lunch (on your own)
01:00 - 02:15 Lecture 10: Demography Inference( Shyam Gopalakrishnan)
02:30 - 04:00 Computer exercises X
04:15 - 05:00 Research lecture by Garrett Hellenthal
Inferring overlapping admixture events among human populations
05:00 - ? Farewell drinks
Evaluation
Participants who have participated actively in all parts of the course and completed all exercises satisfactorily will be awarded a certificate of completion at the end of the course. The work load corresponds to 4 ECTS points. Note that this workload includes one week of preparation. Reading material for this is available in the above course program.